Contacts of the helix formed by residues 563 - 580 (chain P) in PDB entry 1HI0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 563 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P PHE* 3.3 45.3 - - + -
78P ASN* 4.0 23.8 - - + +
80P VAL* 3.4 29.4 - - + -
84P PHE* 4.3 6.3 - - + -
518P ILE* 4.4 12.8 - - + -
561P CYS* 3.3 1.5 - - - -
562P PRO* 1.3 79.5 - - + +
564P TYR* 1.3 68.9 + - - +
565P SER 3.5 1.3 - - - -
566P ASP* 3.2 13.4 + - + +
567P VAL* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 564 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518P ILE* 4.3 11.0 - - + -
521P MET* 4.0 13.7 - - + -
554P MET* 3.3 28.9 - - + +
555P LYS* 3.0 60.5 + - + +
558P TYR* 3.7 24.7 - - + +
559P GLY* 3.7 17.0 - - - +
561P CYS* 3.1 18.4 + - - +
562P PRO 3.5 1.0 + - - -
563P ILE* 1.3 79.1 - - - +
565P SER* 1.3 77.4 + - - +
567P VAL* 2.8 11.3 + - - +
568P LEU* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 565 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555P LYS* 5.7 1.2 + - - -
563P ILE 3.5 0.4 - - - -
564P TYR* 1.3 87.0 - - - +
566P ASP* 1.3 68.5 + - - +
568P LEU* 3.4 8.1 + - - +
569P GLU* 3.1 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 566 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P PHE* 3.6 35.5 - - + -
562P PRO 4.4 3.3 - - - +
563P ILE* 3.4 22.0 - - - +
564P TYR 3.1 0.4 - - - -
565P SER* 1.3 79.0 - - - +
567P VAL* 1.3 58.2 + - - +
569P GLU* 3.2 10.0 + - - +
570P ALA* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 567 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P LEU* 4.0 22.4 - - + -
84P PHE* 5.1 0.7 - - + -
518P ILE* 3.9 21.8 - - + -
521P MET* 3.6 25.4 - - + -
522P LEU* 4.1 15.7 - - + -
563P ILE* 3.0 28.2 + - + +
564P TYR 2.8 14.1 + - - +
566P ASP* 1.3 72.8 - - + +
568P LEU* 1.3 53.5 + - - +
570P ALA* 2.9 8.6 + - - +
571P ILE* 2.7 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521P MET* 4.9 4.9 - - + -
525P GLN* 5.6 0.2 - - - +
551P TRP* 4.1 13.5 - - + -
554P MET* 3.8 30.3 - - + -
564P TYR* 3.1 57.6 + - + +
565P SER* 3.8 9.6 - - - +
567P VAL* 1.3 76.2 - - - +
569P GLU* 1.3 58.2 + - + +
571P ILE* 3.3 17.5 + - + +
572P GLU* 2.8 30.4 + - - +
583P TYR* 5.8 1.3 - - + -
584P ARG* 5.4 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 569 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565P SER* 3.1 22.8 + - - +
566P ASP* 3.4 10.3 - - - +
568P LEU* 1.3 74.9 - - + +
570P ALA* 1.3 65.9 + - - +
572P GLU* 3.3 7.5 + - - +
573P ARG* 2.9 26.2 + - - +
584P ARG* 6.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 570 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU* 3.9 17.9 - - + -
60P TYR* 3.9 26.0 - - + -
61P LEU* 4.0 11.0 - - + -
566P ASP 2.8 17.8 + - - +
567P VAL 3.4 7.2 - - - +
569P GLU* 1.3 71.5 - - - +
571P ILE* 1.3 58.2 + - - +
573P ARG* 3.3 14.0 + - - +
574P CYS* 2.9 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 571 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 3.8 7.9 - - + -
57P LEU* 3.7 25.8 - - + -
521P MET* 4.9 3.1 - - + -
522P LEU* 4.0 10.1 - - + -
525P GLN* 4.5 9.4 - - - +
526P PHE* 3.6 30.1 - - + -
567P VAL* 2.7 30.9 + - + +
568P LEU* 3.4 18.6 - - + +
570P ALA* 1.3 69.6 - - - +
572P GLU* 1.3 69.0 + - - +
573P ARG 3.0 0.3 + - - -
574P CYS 3.0 1.4 + - - -
575P TRP* 2.7 26.9 + - - +
583P TYR* 3.4 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 572 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568P LEU 2.8 21.1 + - - +
569P GLU* 3.5 9.0 - - - +
571P ILE* 1.3 75.9 - - - +
573P ARG* 1.3 58.4 + - - +
575P TRP* 3.8 1.6 - - - +
576P TRP* 3.1 38.8 + - + +
582P SER* 3.0 34.6 + - - -
583P TYR* 3.1 8.9 + - - +
584P ARG* 2.9 58.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 573 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLU* 3.7 21.2 + - - +
60P TYR* 3.1 55.1 + - - +
569P GLU 2.9 16.3 + - - +
570P ALA* 3.3 9.4 - - - +
572P GLU* 1.3 78.6 - - - +
574P CYS* 1.3 68.9 + - - +
576P TRP* 2.8 24.4 + - - +
577P ASN* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 574 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P PHE* 3.5 21.9 - - + +
56P GLU* 3.4 41.7 - - - +
57P LEU* 3.9 24.7 - - + +
60P TYR* 5.2 0.7 - - - -
570P ALA 2.9 22.4 + - - +
573P ARG* 1.3 86.9 - - - +
575P TRP* 1.3 60.3 + - - +
577P ASN* 3.4 5.8 + - - +
578P ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 575 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P TYR* 5.5 2.2 - + - -
43P LEU* 4.4 9.0 - - + -
50P PHE* 3.9 25.6 - + - -
53P PHE* 3.5 27.3 - + + -
526P PHE* 3.9 6.7 - + - -
571P ILE 2.7 20.8 + - - +
572P GLU 3.8 4.0 - - - +
574P CYS* 1.3 70.7 - - - +
576P TRP* 1.3 62.0 + - - +
578P ALA 4.4 0.2 - - - +
579P PHE* 2.8 73.1 + + + +
580P GLY 3.8 0.2 + - - -
581P GLU* 3.4 26.1 + - - +
582P SER 4.6 0.8 + - - -
583P TYR* 3.5 50.6 - + + +
586P TYR* 3.9 31.4 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 576 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E T 6.3 3.1 - + - -
572P GLU* 3.1 27.8 + - + +
573P ARG* 2.8 13.8 + - - +
575P TRP* 1.3 77.7 - - - +
577P ASN* 1.3 63.5 + - - +
580P GLY* 2.7 61.3 + - - +
581P GLU* 3.1 33.6 + - - -
582P SER* 3.6 8.4 - - - +
26Q GLN* 4.1 23.6 - - + -
30Q ARG* 4.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 577 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLU* 3.0 36.3 + - - +
573P ARG* 3.1 27.4 + - - +
574P CYS* 3.5 6.8 - - - +
576P TRP* 1.3 79.7 - - - +
578P ALA* 1.3 61.9 + - + +
580P GLY 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 578 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P ARG* 3.3 48.1 - - - +
52P SER* 5.0 5.8 - - - +
53P PHE* 3.6 17.9 - - + +
56P GLU* 5.8 0.4 - - - +
574P CYS 3.0 17.6 + - - +
576P TRP 3.0 0.2 - - - -
577P ASN* 1.3 80.4 - - - +
579P PHE* 1.3 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 579 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P LEU* 4.8 13.7 - - + -
49P ARG* 3.4 49.1 - - + +
50P PHE* 3.6 33.4 - + + -
53P PHE* 4.3 6.3 - - + -
575P TRP* 2.8 72.4 + + + +
578P ALA* 1.3 85.9 - - + +
580P GLY* 1.3 64.8 + - - +
581P GLU* 3.2 18.0 - - + +
33Q LYS* 3.8 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 580 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576P TRP* 2.7 48.0 + - - -
577P ASN 4.6 0.4 + - - -
578P ALA 3.8 0.4 - - - -
579P PHE* 1.3 74.0 - - - +
581P GLU* 1.3 64.0 + - - +
30Q ARG* 3.8 20.1 + - - -
33Q LYS* 4.4 8.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il